Merge pull request #1190 from galaxyproject/trusted-tool-updates-1763200943

mvdbeek · web-flow · commit e37630b9f962 · 2025-11-17T20:16:59.000+01:00
Update all repos 2025-11-15
diff --git a/scripts/fix_lockfile.py b/scripts/fix_lockfile.py
@@ -94,7 +94,7 @@ def update_file(fn, install_repository_dependencies, install_resolver_dependenci
 
 if __name__ == '__main__':
     parser = argparse.ArgumentParser()
-    parser.add_argument('--no-install-repository-dependencies', action='store_true', default=False,
+    parser.add_argument('--no-install-repository-dependencies', action='store_true', default=True,
                         help="Don't install TS repository dependencies")
     parser.add_argument('--no-install-resolver-dependencies', action='store_true', default=True,
                         help="Don't install tool dependencies via Galaxy dependency resolver (e.g. conda)")
diff --git a/usegalaxy.org/annotation.yml.lock b/usegalaxy.org/annotation.yml.lock
@@ -612,5 +612,6 @@ tools:
   revisions:
   - 59d308975e63
   - 6d5c8a6ceea0
+  - eaa563bd535a
   tool_panel_section_id: annotation
   tool_panel_section_label: Annotation
diff --git a/usegalaxy.org/assembly.yml.lock b/usegalaxy.org/assembly.yml.lock
@@ -358,6 +358,7 @@ tools:
   - 511e5e3cd55e
   - 79b48f02db49
   - 8fef980d48b5
+  - 9c942221e135
   - c6cec5ab35c1
   - dfb8a4497339
   tool_panel_section_id: assembly
@@ -366,6 +367,7 @@ tools:
   owner: iuc
   revisions:
   - 0a10fddd97d2
+  - 0cc7a80463b9
   - 26f2fe7e53a1
   - 44c66e8d21e6
   - 6c571966cfb9
diff --git a/usegalaxy.org/convert_formats.yml.lock b/usegalaxy.org/convert_formats.yml.lock
@@ -11,6 +11,7 @@ tools:
   - 767943cd85bf
   - 7ecb45126cd2
   - b226e0c805a5
+  - f287fbd75138
   - f5792425ea50
   tool_panel_section_id: convert_formats
   tool_panel_section_label: Convert Formats
@@ -259,6 +260,7 @@ tools:
   - 65a69de1e294
   - 66617be450bd
   - 8d6686664021
+  - 9f1c8dc0253e
   - a7387ce2a8ca
   - bbdc53e9b559
   - c6b5c2975e51
@@ -277,6 +279,7 @@ tools:
   - bbbcee71e70e
   - def7a82d23e1
   - f3233d395549
+  - f4f71128f097
   tool_panel_section_id: convert_formats
   tool_panel_section_label: Convert Formats
 - name: ucsc_maftoaxt
diff --git a/usegalaxy.org/data_managers.yml.lock b/usegalaxy.org/data_managers.yml.lock
@@ -115,6 +115,7 @@ tools:
   - 1e34d2e3d285
   - 201eff2131d6
   - 539b008cfe1c
+  - 54871a78828e
   - 8c533e19b697
   - 90b4d4f0a3a4
   - e4b4837f06f5
@@ -124,6 +125,7 @@ tools:
 - name: data_manager_build_bracken_database
   owner: iuc
   revisions:
+  - 174a754bd3b6
   - 5c8a23ccb14a
   - 84cc0dc92b0c
   tool_panel_section_id: data_managers
diff --git a/usegalaxy.org/fasta_fastq.yml.lock b/usegalaxy.org/fasta_fastq.yml.lock
@@ -23,6 +23,7 @@ tools:
   - 660cffd8d92a
   - 80766b36005d
   - 8c0175e03cee
+  - 8e264b67a8c0
   - 944ae523bacb
   - aa784cb3810d
   - b1c926deaa2d
@@ -60,6 +61,7 @@ tools:
   - dbf9c561ef29
   - dbfc505896e9
   - e25816738ef3
+  - f875da9d433c
   tool_panel_section_id: fasta_fastq
   tool_panel_section_label: FASTA/FASTQ
 - name: fastx_trimmer
diff --git a/usegalaxy.org/get_data.yml.lock b/usegalaxy.org/get_data.yml.lock
@@ -76,6 +76,7 @@ tools:
   - 21a560af5913
   - 2e297d531259
   - 34758ab8aaa4
+  - 4edfc76f8a29
   - 7863f1abcdda
   - 9aaa46d45472
   tool_panel_section_id: get_data
@@ -91,6 +92,7 @@ tools:
 - name: iedb_api
   owner: iuc
   revisions:
+  - 1911ec100221
   - 7ed6dda64a81
   tool_panel_section_id: get_data
   tool_panel_section_label: Get Data
@@ -111,6 +113,7 @@ tools:
   owner: iuc
   revisions:
   - 3f1ee30e39e9
+  - 41635d6d4738
   - 5e7401777990
   tool_panel_section_id: get_data
   tool_panel_section_label: Get Data
diff --git a/usegalaxy.org/graph_display_data.yml.lock b/usegalaxy.org/graph_display_data.yml.lock
@@ -287,6 +287,7 @@ tools:
   owner: iuc
   revisions:
   - 0a10fddd97d2
+  - 0cc7a80463b9
   - 26f2fe7e53a1
   - 44c66e8d21e6
   - 6c571966cfb9
@@ -359,6 +360,7 @@ tools:
   - d08080933718
   - dc3fe98e7b37
   - e188a9d25ed2
+  - e237edee9a53
   - ed3a21033188
   tool_panel_section_id: graph_display_data
   tool_panel_section_label: Graph/Display Data
diff --git a/usegalaxy.org/hicexplorer.yml.lock b/usegalaxy.org/hicexplorer.yml.lock
@@ -66,6 +66,33 @@ tools:
   - f881c94fb3b3
   tool_panel_section_id: hicexplorer
   tool_panel_section_label: HiCExplorer
+- name: hicexplorer_chicqualitycontrol
+  owner: bgruening
+  revisions:
+  - 9ea228a9afc8
+  - a63e9713c39d
+  - b892fa1fcaec
+  - f6a169b5e43b
+  tool_panel_section_id: hicexplorer
+  tool_panel_section_label: HiCExplorer
+- name: hicexplorer_chicsignificantinteractions
+  owner: bgruening
+  revisions:
+  - 45a386d18509
+  - 640e0e45518a
+  - f8320df1866b
+  - ff1af7bac1cb
+  tool_panel_section_id: hicexplorer
+  tool_panel_section_label: HiCExplorer
+- name: hicexplorer_chicviewpoint
+  owner: bgruening
+  revisions:
+  - 37125838e360
+  - 40fee49bc6c3
+  - c4ed35f4f77f
+  - f881c94fb3b3
+  tool_panel_section_id: hicexplorer
+  tool_panel_section_label: HiCExplorer
 - name: hicexplorer_chicviewpointbackgroundmodel
   owner: bgruening
   revisions:
diff --git a/usegalaxy.org/image_manipulation.yml.lock b/usegalaxy.org/image_manipulation.yml.lock
@@ -21,5 +21,6 @@ tools:
   owner: bgruening
   revisions:
   - 5c7e14cbff16
+  - 704eca42732d
   tool_panel_section_id: image_manipulation
   tool_panel_section_label: Image Manipulation
diff --git a/usegalaxy.org/interactive_tools.yml.lock b/usegalaxy.org/interactive_tools.yml.lock
@@ -26,5 +26,6 @@ tools:
   owner: rheiland
   revisions:
   - b670740cf3f7
+  - dd051f391a2c
   tool_panel_section_id: interactive_tools
   tool_panel_section_label: Interactive Tools
diff --git a/usegalaxy.org/machine_learning.yml.lock b/usegalaxy.org/machine_learning.yml.lock
@@ -17,6 +17,7 @@ tools:
   - 209b663a4f62
   - 4bd75b45a7a1
   - ba45bc057d70
+  - e7dd78077b72
   - f6a65e05d6ec
   tool_panel_section_id: machine_learning
   tool_panel_section_label: Machine Learning
@@ -39,6 +40,7 @@ tools:
   - ccd798db5abb
   - e2a6fed32d54
   - e674b9e946fb
+  - f07850192bc2
   - f4cb41f458fd
   tool_panel_section_id: machine_learning
   tool_panel_section_label: Machine Learning
diff --git a/usegalaxy.org/mapping.yml.lock b/usegalaxy.org/mapping.yml.lock
@@ -11,6 +11,7 @@ tools:
   - 8a7462c0ac14
   - a07a2d9ddd42
   - a287431cdf4f
+  - d3ece1957fdb
   - d8b6f0adaa79
   - f9b72a376ec9
   - fb4975b507c6
@@ -102,6 +103,7 @@ tools:
   - 11a0d50a54e6
   - 1f06dccdc5d1
   - 3f4d6399997b
+  - 539de907fd99
   - 53c0b7a1a0c3
   - 5cc34c3f440d
   - 66367287b4e6
diff --git a/usegalaxy.org/metagenomic_analysis.yml.lock b/usegalaxy.org/metagenomic_analysis.yml.lock
@@ -18,6 +18,7 @@ tools:
 - name: diamond
   owner: bgruening
   revisions:
+  - 0cdcf7e99b62
   - 1e3323a44643
   - 20d92dc4c6cb
   - 54f751e413f4
@@ -509,6 +510,7 @@ tools:
   - 1a037928504c
   - 1a6cdf55390f
   - 289b3807e80c
+  - 56ff60ec416d
   - 740fd2d16a28
   - b6897977d13e
   - ec368db926f4
@@ -812,6 +814,7 @@ tools:
   - 3481feabc54e
   - 5029fd9d572e
   - 738474880da8
+  - 9b3e1acc3ad0
   tool_panel_section_id: metagenomic_analysis
   tool_panel_section_label: Metagenomic Analysis
 - name: mapseq
@@ -837,6 +840,7 @@ tools:
   owner: iuc
   revisions:
   - 99ff9221182c
+  - afee33334a63
   - b5a7583b8db0
   - fdb13ee4be38
   tool_panel_section_id: metagenomic_analysis
@@ -876,6 +880,7 @@ tools:
   revisions:
   - 15dba9749732
   - 1d97ddbc3464
+  - 37ab2cfedac4
   - 7834132949bc
   tool_panel_section_id: metagenomic_analysis
   tool_panel_section_label: Metagenomic Analysis
@@ -968,6 +973,13 @@ tools:
   - fac3911ad3b6
   tool_panel_section_id: metagenomic_analysis
   tool_panel_section_label: Metagenomic Analysis
+- name: cami_amber_convert
+  owner: iuc
+  revisions:
+  - 848594e0be6a
+  - fac3911ad3b6
+  tool_panel_section_id: metagenomic_analysis
+  tool_panel_section_label: Metagenomic Analysis
 - name: cami_amber
   owner: iuc
   revisions:
diff --git a/usegalaxy.org/nanopore.yml.lock b/usegalaxy.org/nanopore.yml.lock
@@ -134,6 +134,7 @@ tools:
   owner: iuc
   revisions:
   - 0f5f4a208660
+  - 16fc9856b20a
   - 19f3b583a9b3
   - 222669c4afb6
   - 9fb055604648
@@ -159,6 +160,7 @@ tools:
   - eb1f4ba66dc6
   - fa11aa8103b2
   - fbf007713188
+  - fc1f197b33ec
   tool_panel_section_id: nanopore
   tool_panel_section_label: Nanopore
 - name: medaka_variant_pipeline
@@ -186,6 +188,7 @@ tools:
   - b35de691c42c
   - cb34f00cc10f
   - d915879a88bc
+  - d9b6a4615626
   - fc8804320156
   tool_panel_section_id: nanopore
   tool_panel_section_label: Nanopore
diff --git a/usegalaxy.org/proteomics.yml.lock b/usegalaxy.org/proteomics.yml.lock
@@ -150,6 +150,7 @@ tools:
   - 048390db1932
   - 2e667f0ec33c
   - 3f947afe3f71
+  - da1531027506
   - da9ebef968bd
   - e969a182e3cb
   - ef46866326ef
@@ -200,6 +201,7 @@ tools:
 - name: reactome_cli
   owner: paul_wolfe
   revisions:
+  - 6cdacc26e8f4
   - 6dba39f7916f
   - d965cc86f7f5
   tool_panel_section_id: proteomics
diff --git a/usegalaxy.org/qiime2.yml.lock b/usegalaxy.org/qiime2.yml.lock
diff --git a/usegalaxy.org/rna_analysis.yml.lock b/usegalaxy.org/rna_analysis.yml.lock
diff --git a/usegalaxy.org/rna_seq.yml.lock b/usegalaxy.org/rna_seq.yml.lock
diff --git a/usegalaxy.org/sam_bam.yml.lock b/usegalaxy.org/sam_bam.yml.lock
diff --git a/usegalaxy.org/single_cell.yml.lock b/usegalaxy.org/single_cell.yml.lock
diff --git a/usegalaxy.org/statistics.yml.lock b/usegalaxy.org/statistics.yml.lock
diff --git a/usegalaxy.org/text_manipulation.yml.lock b/usegalaxy.org/text_manipulation.yml.lock
diff --git a/usegalaxy.org/virology.yml.lock b/usegalaxy.org/virology.yml.lock
